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Intramolecular interactions are key factors for constructing the secondary conformations of biomolecules and they are also vital for biomolecular functions. Their effect on the surface-enhanced Raman spectroscopy (SERS) spectra is also important for reliable label-free detection. The current work focuses on three GCGC-quadruplexes as model molecules for SERS studies, which contain both the G-quartet and the GCGC-quartet. Their spectra are compared with the ones of the G-quadruplex and the duplex. The present work presents the specific effect of intramolecular interactions, including various Watson–Crick and Hoogsteen hydrogen bonds as well as base stacking, on the SERS signals of closely-related secondary conformations. The overall results indicated a significant influence on the direct label-free detection of DNA molecules and the SERS capability for secondary structural analysis. [ABSTRACT FROM AUTHOR]

In this work, the effects of terminal adenines on the formation and stability of tetramolecular G-quadruplexes (G4s) have been studied by electrospray ionization mass spectrometry (ESI-MS), UV, CD and NMR spectroscopy. Several evidences suggested that the sequences d(AG n A) (n = 4 or 5) form stable uncompleted tetramolecular G4 at acidic condition which is different from the canonical one in the neutral condition. In addition, hydrolysis of guanine has also been observed in acidic condition that may occur for unpaired strands rather than in complete G4. Thus, a new G4 topology containing incomplete G-quartet is proposed that is very stable and particularly presents in acidic ammonium ions solution. The information presented in this study provides the new insight on the polymorphism of G4s in acidic environment, which may help understand of the special role of adenines on the formation of G4s. • A stable slipped tetramolecular G-quadruplex formed by d(AG n A) was proposed. • The hydrolysis of purines in G-quadruplex was observed by mass spectrometry. • The results give a new insight into the association polymorphism of G-quadruplex. [ABSTRACT FROM AUTHOR]

• A label-free and dye-free strategy for sensitive DNA detection has been developed based on self-fluorescent G-quadruplex. • The method allows quantification of DNA without dyes, making the analysis economically and environmentally friendly. • The proposed signal output owns potential for real sample analysis for its biocompatibility and resistance to DNAzyme. The intrinsic fluorescence of the interlocked bimolecular DNA G-quadruplex (93del4T) was utilized to achieve label-free and non-toxic detection of target DNA. The designed probe consists of a single stranded DNA template that hybridizes with the sequence of 93del4T at 5′ end forming partial complementary duplex and leaving single strand overhang at 3′ terminus to recognize target DNA molecule. Once the target DNA hybridizes with the probe to form another part of duplex at 3′ terminus, exonuclease Ⅲ will catalyze the stepwise removal of nucleotides from the blunt 3′ terminus, consecutively liberating the target DNA and the sequence of 93del4T. The released target DNAs can recycle to bind more probes and release more 93del4T that can fold into G-quadruplexes to amplify fluorescence signals. As a result, quantitative detection of the target DNA in human serum has been achieved according to fluorescent signal intensities. In comparison to other methods, this strategy is simple, rapid, inexpensive and toxic free. [ABSTRACT FROM AUTHOR]

[Display omitted] • Three types of DNA nanogels were assembled by the branched DNA units. • SERS has been successfully exploited for the structural analysis of DNA nanogels. • The mechanism for enhancing the SERS signal of DNA gels has been suggested. The direct characterization of DNA nanogels at the atomic level is desirable and of great significance, however, has been challenging because of structural complexity and the larger size of nanogels. Herein, we demonstrated a simple, sensitive and reliable SERS (Surface-enhanced Raman spectroscopy)-based approach towards direct monitoring microstructures, such as three types of nanogels crosslinked by DNA G-quadruplex, i-motif and GC duplex. The achievement is attributed to the detection of featured Raman bands corresponding to the formation of Watson-Crick and Hoogsteen hydrogen bonds as well as C·C+ base pairs. Importantly, this work reveals that the silver nanoparticles attaching on the surface of nanogels can form local 'hotspots' and produce high-quality of Raman spectra under the assistance of iodide, aluminum ions and dichloromethane, therefore, shows great potential for wide applications in accurate characterization of various DNA nanostructures. [ABSTRACT FROM AUTHOR]

DNA G-quadruplexes (G4s) formed by guanine(G)-rich sequences show diversity of structural topologies. The detection of structural details is of great significance for understanding of their functions and for the target drug design, but is very challenging. Herein, we demonstrate that the surface-enhanced Raman spectroscopy (SERS) via Ag IANPs as substrates is able to identify the numbers of Adenine (A) located on the G-quartet of the G4s. Eight G4s are selected for SERS studies. Besides the detection of series of characteristic bands indicating the formation of G4s, the intensity of the band represented A base ring breath (ν A , ~733 cm−1) is observed particularly enhanced when there are A bases coplanar with G-quartet, and which is higher than the intensity of the band corresponding to G base ring breath (ν G, ~655 cm−1). Furthermore, the band intensity ratio of ν A to ν G versus the ratio of the numbers of A on the plane to the sum of numbers of A and G shows very good linear relationship. Thus, based on the band intensities of ν A to ν G and their ratio in the SERS spectrum, the G-quadruplexes with or without a coplanar A base and numbers of A bases on the plane of G-quartet can be facilely identified. The method is simple, fast, low cost and sensitive to provide particular details of the structure in aqueous solution, therefore, implies widespread applications. [Display omitted] • The adenine coplanar G-quartet structure in G-quadruplex was studied by SERS. • It was found that the SERS signal of adenine coplanar G-quartet was extra enhanced. • The number of A bases coplanar with G-quartet was quantitatively studied. [ABSTRACT FROM AUTHOR]

Reduced glutathione (GSH) is one of the important antioxidants in the winemaking and aging process and it also regulates the color and flavor of wines. Accurate and rapid quantification of GSH is crucial in wine quality control. In this study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was demonstrated to quantify GSH and oxidized glutathione (GSSG) of wine in a high-throughput way. Quinoline-5,8-dione was used as a label to react with GSH, and the derivative of GSH, glutamate-cysteine-alanine, acted as the internal standard (IS). The quantitative decrease of GSH and the increase in GSSG were detected with a relative standard deviation of ≤ 5%, after the wines were exposed to air from one to seven days, and the concentration changes of GSH and GSSG were measured by simple dilution. All the results suggested the feasibility and potential of this method for wider applications in the quantification of GSH and GSSG. [Display omitted] • Rapid high throughput quantitative detection of GSH in wine based on MALDI-TOF MS. • The relative standard deviation (RSD) is < 5% and the relative error (RE) is < 1%. • Method can be used for rapid monitoring of changes of GSH and GSSG content in wine. [ABSTRACT FROM AUTHOR]